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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTGCAGTCTGTGCTGATGATCCTGAGTACAAGCATTACAACGATATCAAGGACCTCCCACCTCACCGCTTAGCTGAAATCAGGCGTTTCTTCGAGGACTgtatccttttaatttattgctcttaatgtacttgttctatttgcattcatagagcataaaatattcatggaactctactgaaacaagctcagctagcttc...

Basic information

species Oryza sativa
transcript LOC_Os01g74350.1
intron # 8
splice site 5'
intron type U12 (go to U12 genes for details)

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g74350.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G137930_T02 (Zea mays), 5'ss of exon 7
ATTGCAGTCTGTGCTGATGATCCTGAGTACAAGCATTACAACGATATCAAGGACCTCCCACCTCACCGCTTAGCTGAAATCAGGCGTTTCTTCGAGGACTgtatccttttaatttattgctcttaatgtacttgttctatttgcattcatagagcataaaatattcatggaactctactgaaacaagctcagctagcttc
|||||||| || ||||||||||| ||||||| ||||||||| ||||||||||| ||||||||||||||||| |||||||||||||| ||||||||||||||||||||||| ||   |      || |           |     | ||    |  | | ||  |   ||    | |  | |  |    | || |   || 
ATTGCAGTGTGCGCTGATGATCCCGAGTACAGGCATTACAATGATATCAAGGAGCTCCCACCTCACCGCTTGGCTGAAATCAGGCGCTTCTTCGAGGACTgtatcctttttatgattcatcagtatttcgtcctgctaaccaagagtctagtactacataaagtgattgctgttttgatcatgcttaataagttctttta

upper sequence: LOC_Os01g74350.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GLYMA13G19500.1 (Glycine max), 5'ss of exon 7
ATTGCAGTCTGTGCTGATGATCCTGAGTACAAGCATTACAACGATATCAAGGACCTCCCACCTCACCGCTTAGCTGAAATCAGGCGTTTCTTCGAGGACTgtatcctttt----aattt---attgctcttaat--gtacttgttctattt--gcattcatagagca-taaaatattcatggaac-tctactgaaacaagctcagctagcttc------------------------------
||||| ||||||||||||||||||||||| | ||||||||| ||||||||||| || || || ||||| |||||||||||  | |||||||| || || ||||||||||     |||||   | ||   ||  |  | ||||  | ||| |  ||||  | | | ||   |||||  || | | | | |  ||   || |   |   |   |                               
ATTGCTGTCTGTGCTGATGATCCTGAGTATAGGCATTACAATGATATCAAGGAGCTTCCTCCACACCGTTTAGCTGAAATTCGTCGTTTCTTTGAAGATTgtatcctttccaagaatttcaaaatgtgtttgttcagcacttcctatatgttagcatctacataacagcgaaatacacaagtatcatttggtgcgccatgtaaaatcaaactatttttgtgtttttcttaataaaggaattag

upper sequence: LOC_Os01g74350.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GLYMA19G35710.1 (Glycine max), 5'ss of exon 9
ATTGCAGTCTGTGCTGATGATCCTGAGTACAAGCATTACAACGATATCAAGGACCTCCCACCTCACCGCTTAGCTGAAATCAGGCGTTTCTTCGAGGACTgtatccttttaa----ttta----------ttgctcttaa-----tgtacttgtt-----ctatttgcattcatagagcataaaatattcatggaactctac--tgaaacaagctcagctagcttc------------------------------
||||| ||||||||||||||||||||||| |  |||||||| |||||||| || || || || || || |||||||||||  | ||||| || || ||||||||||||  ||    | ||          ||| | || |     | ||||||||     |||   ||||    | | ||| |||||    |||  || | |  || | || |   |   |   |                               
ATTGCTGTCTGTGCTGATGATCCTGAGTATAGACATTACAATGATATCAAAGAGCTTCCTCCACATCGTTTAGCTGAAATTCGTCGTTTTTTTGAAGACTgtatccttccaagaattctaattccaatgtttgattttcaaattttctacttgttaacgtctacaggcatgttgaaatcatgaaatacat-tggtccttttcagtgcagcatgtgaaataaatgttatagtttgttttccttcataaaggatttag

upper sequence: LOC_Os01g74350.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GLYMA03G33000.6 (Glycine max), 5'ss of exon 9
ATTGCAGTCTGTGCTGATGATCCTGAGTACAAGCATTACAACGATATCAAGGACCTCCCACCTCACCGCTTAGCTGAAATCAGGCGTTTCTTCGAGGACTgtatccttt---------------taatttattgctcttaa----tgtacttgtt-----ctatttgcattcatagagcataaaatattcatggaactctac--tgaaacaagctcagctagcttc-----------------------------
||||| ||||||||||||||||| |||||    |||||||| ||||||||||| || || || || || |||||||||||  | ||||| || || ||||||||||||                |||| | | | | | ||    | || |||||     |||| | |||   || | ||| ||||     |||  || | |  || | || |   |   |   |                              
ATTGCTGTCTGTGCTGATGATCCCGAGTATCGACATTACAATGATATCAAGGAGCTTCCTCCACATCGTTTAGCTGAAATTCGTCGTTTTTTTGAAGACTgtatccttccaaaaatgcaaattctaatgtttggttttcaaattttctatttgttaacgtctatgtacatgattaaatcatgaaatgcgt-tggtccttttcagtgcagcatgtgaaatgaatgttattgttgttttccttcataaaggatttag

upper sequence: LOC_Os01g74350.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GLYMA10G05130.1 (Glycine max), 5'ss of exon 7
ATTGCAGTCTGTGCTGATGATCCTGAGTACAAGCATTACAACGATATCAAGGACCTCCCACCTCACCGCTTAGCTGAAATCAGGCGTTTCTTCGAGGACTgtatcctttt----aattt---attgctcttaat--gtacttgttctattt--gcattcatagagcataaaatattcatggaactctactgaaacaagctcagctagcttc-------------------
||||| ||||||||||||||||||||||| | ||||||||| |||||||||||||| || |||||||| |||||||||||  | |||||||| || || ||||||||||     |||||   | ||   ||  |  ||||||  | ||| |  ||||  ||| ||    ||  |||    |  |  ||   || ||| ||    ||  ||                    
ATTGCTGTCTGTGCTGATGATCCTGAGTATAGGCATTACAATGATATCAAGGACCTTCCTCCTCACCGTTTAGCTGAAATTCGTCGTTTCTTTGAAGATTgtatcctttccaagaatttcaaaatgtgtttgttcagtacttcctatatgttagcatctatataggt--aatcatttggcgtgccatataaaatcaaactattttatgttttccttaataaaggaattag

upper sequence: LOC_Os01g74350.1 (Oryza sativa), 5'ss of exon 8
lower sequence: Vv08s0040g02470.t01 (Vitis vinifera), 5'ss of exon 7
ATTGCAGTCTGTGCTGATGATCCTGAGTACAAGCATTACAACGATATCAAGGACCTCCCACCTCACCGCTTAGCTGAAATCAGGCGTTTCTTCGAGGACTgtatccttttaa---tttattgctcttaatgtac-ttgttctatttgcattcatagagcataaaatattcatggaactctactgaaacaagctcagctagcttc-------------------------------------------------
|||||||| |||||||||||||||||||||   || ||||  |||||||| || ||||| || ||||| || ||||| ||| | |||||||| || || ||||||||| |||   ||  |    ||||    ||  |  | ||     |||| |  ||||||   |  | |    |||    |         | | ||    ||                                                 
ATTGCAGTTTGTGCTGATGATCCTGAGTACCGACACTACACTGATATCAATGAGCTCCCTCCGCACCGTTTGGCTGAGATCCGCCGTTTCTTTGAAGATTgtatccttctaaaaattcttaatccttagcaaacactagtttaaaacgattcttcaagcatactgtccttaaaatacttgtttatttttttataatctcaaatctagaaaattggatctaaatcatcctttttttccttaataaaccaatcag

upper sequence: LOC_Os01g74350.1 (Oryza sativa), 5'ss of exon 8
lower sequence: PP1S142_132V6.1 (Physcomitrella patens), 5'ss of exon 4
ATTGCAGTCTGTGCTGATGATCCTGAGTACAAGCATTACAACGATATCAAGGACCTCCCACCTCACCGCTTAGCTGAAATCAGGCGTTTCTTCGAGGACTgta--tccttttaatttatt---gctcttaatgtacttgttctatttgcattcatagagcataaaatattcatggaactctactgaaacaagctcagctagcttc-------------------------------------------------------------------------------------
|| || ||||||||||| ||||| ||||||| ||| | ||| || |||||||| ||||| || ||||| || ||||| ||| | || || || ||||||||||  || |||| ||   ||    |   |   | |||  ||   |||   |   |||    |    | ||  | |   | |       |    |  |||    ||                                                                                     
ATCGCTGTCTGTGCTGACGATCCCGAGTACAGGCACTTCAAGGACATCAAGGAACTCCCTCCCCACCGTTTGGCTGAGATCCGTCGGTTTTTTGAGGACTgtaagtcattttcatgcgttcatacctctggcgcactaatttattttttttcggtagttttttttgttttttttgttttttttcctccctgtgtatgctgctgtcatacatcatggattttaatgggtttgttttaggtctattaatatggacattcacttcactgactagcacgcaaccattgttacag

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|86478948|gb|CI121581.1|CI121581
EST:     GGACCTCCCACCTCACCGCTTAGCTGAAATCAGGCGTTTCTTCGAGGACT                         ACAAGAAGAATGAGAATAAGGAGGTGGCTGTCAACGACTTCATGCCTGCCA
genomic: GGACCTCCCACCTCACCGCTTAGCTGAAATCAGGCGTTTCTTCGAGGACTgtatcctttt ... ggtaaaatagACAAGAAGAATGAGAATAAGGAGGTGGCTGTCAACGACTTCATGCCTGCCA
EST: gi|88510233|gb|CI437739.1|CI437739
EST:     GGACCTCCCACCTCACCGCTTAGCTGAAATCAGGCGTTTCTTCGAGGACT                         ACAAGAAGAATGAGAATAAGGAGGTGGCTGTCAACGACTTCATGCCTGCCA
genomic: GGACCTCCCACCTCACCGCTTAGCTGAAATCAGGCGTTTCTTCGAGGACTgtatcctttt ... ggtaaaatagACAAGAAGAATGAGAATAAGGAGGTGGCTGTCAACGACTTCATGCCTGCCA
EST: gi|29621784|gb|CB626795.1|CB626795
EST:     GGACCTCCCACCTCACCGCTTAGCTGAAATCAGGCGTTTCTTCGAGGACT                         ACAAGAAGAATGAGAATAAGGAGGTGGCTGTCAACGACTTCATGCCTGCCA
genomic: GGACCTCCCACCTCACCGCTTAGCTGAAATCAGGCGTTTCTTCGAGGACTgtatcctttt ... ggtaaaatagACAAGAAGAATGAGAATAAGGAGGTGGCTGTCAACGACTTCATGCCTGCCA
EST: gi|88515599|gb|CI443253.1|CI443253
EST:     GGACCTCCCACCTCACCGCTTAGCTGAAATCAGGCGTTTCTTCGAGGACT                         ACAAGAAGAATGAGAATAAGGAGGTGGCTGTCAACGACTTCATGCCTGCCA
genomic: GGACCTCCCACCTCACCGCTTAGCTGAAATCAGGCGTTTCTTCGAGGACTgtatcctttt ... ggtaaaatagACAAGAAGAATGAGAATAAGGAGGTGGCTGTCAACGACTTCATGCCTGCCA
EST: gi|88486325|gb|CI423596.1|CI423596
EST:     GGACCTCCCACCTCACCGCTTAGCTGAAATCAGGCGTTTCTTCGAGGACT                         ACAAGAAGAATGAGAATAAGGAGGTGGCTGTCAACGACTTCATGCCTGCCA
genomic: GGACCTCCCACCTCACCGCTTAGCTGAAATCAGGCGTTTCTTCGAGGACTgtatcctttt ... ggtaaaatagACAAGAAGAATGAGAATAAGGAGGTGGCTGTCAACGACTTCATGCCTGCCA
EST: gi|88485439|gb|CI422710.1|CI422710
EST:     GGACCTCCCACCTCACCGCTTAGCTGAAATCAGGCGTTTCTTCGAGGACT                         ACAAGAAGAATGAGAATAAGGAGGTGGCTGTCAACGACTTCATGCCTGCCA
genomic: GGACCTCCCACCTCACCGCTTAGCTGAAATCAGGCGTTTCTTCGAGGACTgtatcctttt ... ggtaaaatagACAAGAAGAATGAGAATAAGGAGGTGGCTGTCAACGACTTCATGCCTGCCA

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 25 (upstream exon), 26 (downstream exon)
Score: 1

ATTGCAGTCTGTGCTGATGATCCTGAGTACAAGCATTACAACGATATCAAGGACCTCCCACCTCACCGCTTAGCTGAAATCAGGCGTTTCTTCGAGGACTgtatcctttt ... ggtaaaatagACAAGAAGAATGAGAATAAGGAGGTGGCTGTCAACGACTTCATGCCTGCCACTTCTGCTTATGAGACCATACGCCATTCCAT




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Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATTGCAGTCTGTGCTGATGATCCTGAGTACAAGCATTACAACGATATCAAGGACCTCCCACCTCACCGCTTAGCTGAAATCAGGCGTTTCTTCGAGGACTgtatccttttaatttattgctcttaatgtacttgttctatttgcattcatagagcataaaatattcatggaactctactgaaacaagctcagctagcttc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA